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57 Cards in this Set

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T/F: Of all nature's molecules, nucleic acids are unique in their ability to direct their own replication from monomers.
T/F: Until the 1940s, the heterogeneity and specificity of function of proteins made them a likely candidate for being the basis of inheritance and DNA
When British Frederick Griffith mixed a dead group of the pathogenic strain of pneumonia with an alive group of the non-pathogenic strain, what happened and what was this called?
The non-pathogenic strains all subsequently became pathogenic. Grifith called this "transformation."
What is the official definition of a transformation (separate from the transformation of a normal cell into a cancerous cell as from chapter 12)?
When a change in genotype and then phenotype occurs due to the assimilation of external DNA by a cell
How did Oswald Avery discover that in bacteria the heritable factor that transformed the pneumonia prokaryotes from pathogenic to non pathogenic was DNA?
He had chemicals that inactivated DNA, RNA, and protein, and only when DNA was activated was transformation allowed to occur.
Why did virtually no one care about Oswald's discovery during his time?
Bc most people believed that proteins were more complex & thus the basis of heredity and most people thought human heredity was much different than bacteria heredity
Describe bateriophages, or phages, such as T2, and what they do.
They are viruses that "eat" bacteria and are only composed of DNA and protein. They attach to their host and cause it to produce many many more T2 phages, somehow altering the host's hereditary mechanisms.
Why was the Hershey-Chase experiment so groundbreaking?
Bc the use of radioactive tracers showed that the DNA of a phage entered the host cell and caused the mutation, not the protein. It showed that DNA was the molecular basis of inheritance, at least for viruses.
How did Erwin Chargaff perform an important experiment?
He showed that different species had different percentages of each amount of base pair in their DNA, which gave DNA more credibility as the diverse molecular basis of inheritance.
What was the second important discovery made by Chargoff?
That Adenine and thymine, and then cytosine and guanine are present in equal percentages in all organisms.
How did Watson initially come up with his "two strand" molecule?
He visited the lab of Wilkins and Rosalind franklin and from their crystallography (study of 3-D structures by the use of X-rays) he determined that DNA was helical & (by studying the width of the helix) he found that it was a double stranded, not triple stranded as some people had suggested.
How many layers of base pairs, or rungs of the ladder, are there in each full turn of the helix?
Other than using Rosalind Franklin's crystallography, how else did Watson and Crick basically rip her off?
They used her unpublished report which proved that the phosphate group and sugar were on the outside of the double helix bc they are hydrophilic and base pairs are hydrophobic
How did Watson and Crick know that A didn't pair with A, and so on?
Bc the crystallography suggested that the width of DNA was uniform. A and G are purines & are about twice as long as T and C which are pyrimidines. If A paired with A and T with T, DNA would not be of uniform width
How did Watson and Crick reason that there must be additional specificity in the pairing of nitrogenous bases?
Bc A only forms two hydrogen bonds with T, and G only forms three hydrogen bonds with C; not just any purine can combine with any pyrimidine
When referring to the 5' and 3' ends of DNA, we are talking about the ULTIMATE ends of the sugar, not in between. What does the 5' end have and what does the 3' end have?
5' has the P group, 3' has the OH group.
What is the semi-conservative model and what were the two other possibilities of models proposed before the semi-c was proven?
This model says that one strand of parent DNA molecule and a new complementary strand make up DNA after replication. The conservative model says that the parent molecule is always conserved and somehow binds back up after replication, and the dispersive model says that all four separate strands of DNA have a mixture of old and new DNA.
Matthew Meselson and Franklin Stahl confirmed...
The semi-conservative model of DNA replication
Short stretches of DNA having a specific sequence of nucleotides where the replication of a DNA molecule begins are called...
Origins of replication
T/F: DNA replication proceeds in both directions from the origin of replication in all cells
In eukaryotes, what completes basic DNA replication?
When all the linear replication bubbles keep growing in both directions and the replication forks finally fuse and the bubbles are together, then DNA replication is complete and the old 2 strands of the parent molecule are completely separate
What protein helps unwind and separate the strands of the single DNA molecule at the replication fork?
What molecules bind to the UNPAIRED DNA strands of DNA during replication and stabilizes them?
Single-strand binding proteins
What molecules bind to the full, unseparated strand of DNA ahead of the replication fork? What does it do and why?
The untwisting of DNA at the replication fork causes tighter twisting ahead of the fork, so topoisomerase helps to relieve this strain by breaking, swiveling, etc.
What is an RNA primer, what does it do, and what makes it?
Primase makes the RNA primer, about 10 bases of RNA which INITIATE the copying of DNA. After primase makes the RNA primer and binds it to the DNA molecule with respective base pairs, DNA-bearing enzymes can start the total copying of the DNA.
Describe the structure of a nucleoside triphosphate.
A sugar, a nitrogenous base, and 3 phosphate groups.
Explain what happens when each nucleotide added to a parent strand of DNA for replication comes from a nucleoside.
2 P groups from the nucleoside are lost to form pyrophosphate which is hyrdolyzed in an exergonic reaction which helps fuel the polymerization process of all the new base pairs. The remaining parts of the nucleoside create the single phosphate group, sugar, and base that make up a normal strand of DNA.
In E. coli, what adds a DNA nucleotide to the RNA primer and then continues adding DNA nucleotides along the replication fork?
DNA polymerase III
T/F: Bc of its structure, DNA polymerase can ONLY add nucleosides/nucleotides to a parent strand of DNA in the 5' to 3' direction, which is cool for one direction of the replication fork, but not okay for the other
Bc DNA polymerase can only replicate in the 5' -> 3' direction, and the replication fork goes both ways down the 2 parent strands of a DNA molecule, what is the easy strand called that already goes from the 5' to 3' direction? How many RNA primers are necessary?
The leading strand; only 1 RNA primer is needed
The DNA strand that DNA polymerase III has to replicate AWAY from the replication fork so that it can follow its 5' to 3' direction is called the...
Lagging strand
T/F: The lagging strand is elongated discontinuously in a series of segments
EACH of the 2 DNA strands in a parent DNA molecule has leading and lagging strands. Why?
Because the replication fork goes in BOTH ways, so the 5' -> 3' strand (from top to bottom) will have replication going in both ways when in reality the DNA poly III can only replicate from the 5' to 3' direction
The segments of the lagging strand that are created during replication are called...
Okazaki fragments
After RNA primase primes the individual Okazaki fragments of the lagging strand, what molecule replaces the RNA with copies of DNA, adding them one by one onto the 3' end of the fragment?
DNA polymerase I
Although DNA Poly I replaces the RNA primer with DNA, it cannot join the two Okazaki segments to create a full strand. What ultimately does this?
DNA ligase
What is the "sliding clamp"? What does it do?
The sliding clamp is the protein that follows behind DNA poly III while the poly III adds nucleotides/nucleosides to the parent strand of DNA. It physically moves DNA poly III along the DNA template strand
Why isn't a model of the proteins associated with DNA replication moving along DNA like a railroad track plausible?
Bc all the proteins are actually together in a complex and bc the DNA being replicated is actually "pulled thru" the complex, while the complex remains still and unmoving in the nuclear matrix
If a mismatch pair of nucleotide bases is created during DNA replication and evades the proofreading of the DNA polymerase, what happens and what is important about this?
If this happens, enzymes remove and replace incorrectly paired nucleotides that have resulted in replication errors. These enzymes are important bc genetic defects that lead to their absence has been directly shown to cause colon cancer.
T/F: Bc of spontaneous or environmental mutation factors, the DNA in each cell even before or after replication is constantly monitored and repaired by the cell.
Briefly explain a nucleotide excision repair.
When damage is detected, a nuclease enzyme cuts out one segment of the damaged strand, DNA poly adds new bases, and DNA ligase finally binds the new molecule together.
In what situations are thymine dimers usually created?
They are usually created from damage from UV light
Special, often short, repeating nucleotide sequences at the ends of linear DNA that protect from eventual DNA erosion yet use proteins in order to not trigger damage pathways are called...
If the chromosomes of germ cells became shorter in every cell cycle, essential genes would eventually be missing from the gametes they produce. Why doesn't this actually every occur?
Bc the enzyme telomerase lengthens telomeres in eukaryotic germ cells, which make gametes (sex cells) with telomeres of longest possible length
T/F: Normal shortening of telomeres may protect organisms from cancer by limiting the number of divisions that regular cells can undergo.
T/F: The presence of telomerase in many cancer cells suggests that it (obviously) allows more replication to occur than should be possible and could be the cause of constantly-replicating cancer
The dense region of DNA in a bacterium unlike that of eukaryotic cells is called a nucleoid, and is...
Not bound by a membrane
The complex of DNA and protein that fits into the nucleus through an elaborate, multilevel system of DNA packing is called...
T/F: Although histone proteins are small, their mass is about exactly equivalent to the mass of total DNA in a nucleus
Why do histones readily bind to a linear DNA molecule?
Bc they are positively charged with their amino acids and the P groups on DNA make it negatively charged
Each bead between the 10nm chromatin strands is called a _, the basic unit of DNA packaging.
The "string" between the beads of nucleosomes of chromatin is called...
Linker DNA
T/F: DNA rarely leaves the histone-cluster in a nucleoside
What is the 30nm fiber?
When the nucleosides get together due to the interactions of histone tails and form a big coil of nucleosides and linker DNA
When the 30nm fiber forms loops and is attached to a "chromosome scaffold" made of proteins, this is called...
A looped domain
T/F: The looped domains often lack a definite scaffold but may be attached to the nuclear lamina or the nuclear matrix which helps organize regions of chromatin, and even when chromatin is just in a big heap of DNA individual chromosomes do not become entangled
What is the difference between heterochromatin and euchromatin?
Heterochromatin is the big ball of centromeres and telomeres that heaps up even during interphase and thus cannot usually be used during gene expression. Euchromatin is the rest of the cell's DNA which is not very coiled up during interphase and can thus be used for gene expression